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- PDB-5dmv: Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (... -

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Basic information

Entry
Database: PDB / ID: 5dmv
TitlePolo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)
Components
  • F-box only protein 43
  • Serine/threonine-protein kinase PLK1
KeywordsTRANSFERASE/METAL BINDING PROTEIN / Polo-box / PLK1 / Emi2 / meiosis / TRANSFERASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of cell cycle process / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / negative regulation of meiotic nuclear division ...Polo-like kinase mediated events / Phosphorylation of the APC/C / Phosphorylation of Emi1 / Mitotic Metaphase/Anaphase Transition / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Golgi Cisternae Pericentriolar Stack Reorganization / negative regulation of cell cycle process / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / negative regulation of meiotic nuclear division / Condensation of Prophase Chromosomes / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / protein localization to organelle / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of protein localization to cell cortex / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of meiotic nuclear division / synaptonemal complex disassembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / polo kinase / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / protein localization to nuclear envelope / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / homologous chromosome segregation / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / female meiosis chromosome segregation / nuclear membrane disassembly / synaptonemal complex / anaphase-promoting complex binding / outer kinetochore / condensed chromosome, centromeric region / positive regulation of ubiquitin protein ligase activity / microtubule bundle formation / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic spindle assembly / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic nuclear division / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / spindle midzone / mitotic G2 DNA damage checkpoint signaling / mitotic cytokinesis / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / chromosome, centromeric region / negative regulation of double-strand break repair via homologous recombination / protein localization to chromatin / centriole / regulation of cytokinesis / meiotic cell cycle / spindle microtubule / establishment of protein localization / negative regulation of protein catabolic process / kinetochore / protein destabilization / G2/M transition of mitotic cell cycle / centriolar satellite / spindle / spindle pole / mitotic cell cycle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / midbody / microtubule binding / protein phosphorylation / protein kinase activity / protein ubiquitination / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / negative regulation of apoptotic process / chromatin / magnesium ion binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / IBR domain ...Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / IBR domain / In Between Ring fingers / Arylsulfatase, C-terminal domain / POLO box domain / POLO box domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Serine/threonine-protein kinase PLK1 / F-box only protein 43
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsNamgoong, S.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization.
Authors: Jia, J.L. / Han, Y.H. / Kim, H.C. / Ahn, M. / Kwon, J.W. / Luo, Y. / Gunasekaran, P. / Lee, S.J. / Lee, K.S. / Bang, J.K. / Kim, N.H. / Namgoong, S.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Serine/threonine-protein kinase PLK1
D: F-box only protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1275
Polymers30,9512
Non-polymers1763
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-22 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.627, 63.329, 56.831
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27242.980 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 367-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plk1, Plk / Production host: Escherichia coli (E. coli) / References: UniProt: Q07832, polo kinase
#2: Protein/peptide F-box only protein 43 / Endogenous meiotic inhibitor 2


Mass: 3707.863 Da / Num. of mol.: 1 / Fragment: Emi2 peptide (UNP RESIDUES 146-177) / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8CDI2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10mM MgCl2, 5mM NiCl2, 15% PEG 3350, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.499→28.414 Å / Num. obs: 8266 / % possible obs: 97.9 % / Redundancy: 4 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.499→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.47 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1688refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.499→28.414 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 33.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2909 414 5.01 %Random selection
Rwork0.2117 ---
obs0.2156 8266 94.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.499→28.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 3 38 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131973
X-RAY DIFFRACTIONf_angle_d1.9752673
X-RAY DIFFRACTIONf_dihedral_angle_d14.061733
X-RAY DIFFRACTIONf_chiral_restr0.09307
X-RAY DIFFRACTIONf_plane_restr0.011335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4993-2.86060.33041300.23542471X-RAY DIFFRACTION90
2.8606-3.6030.26791410.22412678X-RAY DIFFRACTION97
3.603-28.41630.29081430.19752703X-RAY DIFFRACTION96

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